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使用色散校正密度泛函理论计算对实验分子晶体结构进行验证。

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

作者信息

van de Streek Jacco, Neumann Marcus A

机构信息

Avant-garde Materials Simulation, Merzhauser Str. 177, D-79100 Freiburg im Breisgau, Germany.

出版信息

Acta Crystallogr B. 2010 Oct;66(Pt 5):544-58. doi: 10.1107/S0108768110031873. Epub 2010 Sep 11.

Abstract

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

摘要

本文描述了一种色散校正密度泛函理论(d-DFT)方法的验证过程,目的是评估实验有机晶体结构的正确性,并增加纯实验数据的信息含量。对2008年8月《晶体学报E辑》中的241个实验有机晶体结构进行了全面的能量最小化处理,包括晶胞参数。对实验晶体结构和最小化后的晶体结构之间的差异进行了统计分析。选择在灵活晶胞参数下进行能量最小化时不包括氢原子的均方根笛卡尔位移作为晶体结构正确性的相关指标。所有241个实验晶体结构都得到了很好的重现:包括16个无序结构在内的241个晶体结构的平均均方根笛卡尔位移仅为0.095 Å(225个有序结构为0.084 Å)。均方根笛卡尔位移大于0.25 Å要么表明实验晶体结构不正确,要么揭示出有趣的结构特征,如异常大的温度效应、建模错误的无序或对称性破缺的氢原子。验证后,该方法应用于九个已知存在歧义或存在细微错误的例子。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6cc0/2940256/8c6cd29fce56/b-66-00544-fig1.jpg

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